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<p class="title1">The Ubbit</p>
<hr
	style="float: left; color: #ABE107; background-color: #ABE107;">
</br>

<p>We propose the widening of the BioBrick standard, not by increasing
the library of components but adding steps in the abstraction hierarchy.
We believe that the tendency of synthetic biology in this decade is
going to be the distribution of complex functions among strains so that
the cells are not overloaded. The rise of the number of communication
substances will limit the number of strains that can remain in the same
environment.That leaves us with the necessity of dividing physically the
strains in different places.</p>

<p>This project pursues the objective of finding a substance that acts
as a link among communities, thus becoming a putative synthetic quorum
sensing system. This substance, the Universal BioBit (Ubbit) shall
fulfill certain requirements: firstly, biosynthesis should be possible;
secondly, it needs to be degraded efficiently; and thirdly, it should
induce the genetic expression of what we want in a target cell. Our
research will assess the behavior of many substances and finally we will
publish the results with a free use license (probably Creative Commons).</p>

<img
	style="margin-left: 150px;" src="images/ubbit.png" />


<p class="title1">Ubbit standard specification</p>
<hr
	style="float: left; color: #ABE107; background-color: #ABE107;">
</br>
<p>We define three levels in the abstraction hierarchy:</p>
<p>
<ul>
	<li><b>Cell level:</b> defined by the BioBrick standard. (Go to the
	parts registry to know the rules)</li>
	<li><b>Community level:</b> defined by Ubbit standard: wire subformat.
	It’s composed by cells connected by wires.</li>
	<li><b>Population level (or super-community level):</b> defined by
	Ubbit standard: Ubbit format. It’s composed by communities connected
	through Ubbit-wires.</li>
</ul>
</p>
<p class="title2">Community level</p>
<p>Here, we have the community as the main entity we want to set to
provide it with differents skills. Is composed by differents cells with
differents behaviours conected through wires. All the behaviours and
wires must have been created using the BioBrick standard.</p>

<div id="wire" style="padding-left: 50px;">
<p class="title3">Wire</p>

<p>A wire is an entity with the ability to connect two differents cells
in a unidirectional way. The information is encoded in a BioBit (bbit
shorted form). A bbit is a pulse of information. It can be a chemical
substance, defining a CBW (Chemical-Based Wire) or light with a specific
wavelenght, defining a LBW (Light-Based Wire).</p>

<p>A wire is composed by three parts:</p>
<div style="padding-left: 30px;">
<p><b>EHW, Emitter Half-Wire</b></p>
<p style="margin-top: -10px;">The Emitter Half-Wire is the minimum set
of genes required to emit a bbit pulse. It is not constitutively
expressed. The nomenclature is: once defined the nature of the bbit, a
for instance, the EHW is noted this way: EHW(a) or E(a). The BioBrick
components of the EHW are [{B0034 + genei}N + B0015] where N is the
number of genes.</p>

<p><b>RHW, Receptor Half-Wire</b></p>
<p style="margin-top: -10px;">The Receptor Half-Wire is the minimum set
of genes required to sense the presence of a specific bbit and a target
promoter. It’s constitutively expressed. The nomenclature is: once
defined the nature of the bbit, a for instance, the RHW is noted this
way: RHW(a) or R(a). The BioBricks components of the RHW are [J23119 +
{B0034 + genei}N + B0015 + TargetPromoter], where N is the number of
genes.</p>

<p><b>SINK</b></p>
<p style="margin-top: -10px;">The Sink is the minimum set of genes
required to degradate a specefic bbit. It’s constitutively expressed.
The nomenclature is: once defined the nature of the bbit, a for
instance, the SINK is noted this way: SINK(a) or S(a). If the SINK is
able to degradate a set of bbits, then separate by commas: SINK(a, b, c,
… ,n, … ,z). You can also note the multiple SINK this way:</p>
<p><img style="margin-left: 200px;" src="images/image00.png"></p>
<p style="margin-top: -10px;">The BioBricks components of the SINK are
[J23119 + {B0034 + genei}N + B0015] where N is the number of genes.</p>
</div>
</div>

<div id="wire" style="padding-left: 50px;">
<p class="title3">Wire Rules:</p>
<ol>
	<li>The wire structure must not be interrupted at all.</li>
	<li>The bbit must not be toxic for the cells in the module media.</li>
	<li>A wire is composed by a EHW, a RHW and a SINK.</li>
	<li>There can be more than one EHW, or RHW or SINK for the same bbit.</li>
</ol>
</div>


<div id="wire" style="padding-left: 50px;">
<p class="title3">The cell</p>
<p>Every cell has a connecting envelope and a logic core.</p>
<div style="padding-left: 30px;">
<p><b>Connecting envelope</b></p>
<p style="margin-top: -10px;">It’s composed by two parts, the Receptor
Envelope which is the set of all the RHWs in the cell, and the Emitter
Envelope, which is the set of all the EHW in the cell.</p>

<p><b>Logic cores</p>
</b>
<p>A logic core is a genetic circuit which is able to carry logic
functions. It must be prepared to receive the information through RHWs
for the inputs bbits and activate EHWs to emit the output bbits. Its
structure it’s not defined in a standardized way.</p>
</div>
</div>
<!--  <h3>Kinectics</h3> Como wire-->

<p class="title2">Population Level</p>
<p>Here, a population is the main entity we want to set to provide it
with differents skills. Is composed by modules, composed by differents
communities with differents behaviours conected through Ubbit wires. All
wires must have the wire format.</p>

<div id="module" style="padding-left: 50px;">
<p class="title3">Modules</p>
<p>A module is a physical entity composed by input and output translator
chambers and the community chamber. The translator chambers are
separated from the community chamber by membranes that only leave the of
pass substances (bbits) but not cells. Translator chambers have another
membrane to the outside of the module, to allow the entrance and exit of
substances in the module. The modules can be connected by this
membranes. Inside the translator chambers there is one translator strain
with the ability to produce a internal communication substance in
presence of Ubbit (inputs), or viceversa (outputs). The translator
strains are noted this way:</p>

<p>Input translator from Ubbit to community a bbit:</p>
<p><img style="margin-left: 210px;" src="images/image01.png"></p>


<p>Output translator from community i bbit to Ubbit:</p>

<p><img style="margin-left: 210px;" src="images/image02.png"></p>
</div>

<div id="ubbitwire" style="padding-left: 50px;">
<p class="title3">Ubbit wire</p>
<p>Ubbit wire is a wire (Ubbit comes from Universal BioBit) at first.
The special characteristic of this wire is about the molecule nature: it
must be different from the bbits inside the community, because its SINK
must be specific only for it. The Ubbit SINK, S(Ubbit), must be located
in the community chamber. And the Ubbit wire must run in a wide variety
of species, and the version of the standard is defined by the number of
different genus that are able to support the Ubbit wire. Ubbit 3.0 would
be a wire that works in <i>E. coli</i>, <i>B. subtilis</i> and <i>S.
cerevisiae</i>.</p>
</div>
<div id="communchamber" style="padding-left: 50px;">
<p class="title3">Community chamber</p>
<p>This is the space that contains the community, defined by the
community level rules. The SINKs for the community bbits must be located
in the translator chambers.</p>
</div>
<div id="trnadc" style="padding-left: 50px;">
<p class="title3">Transducer input modules</p>
<p>They are modules with the ability to sense a environmental variable
(light, chemical compound, temperature, radiation,... ) and emit Ubbit.
It’s composed by the input sensor device coupled to a E(Ubbit).</p>
</div>
<div id="trndoutmod" style="padding-left: 50px;">
<p class="title3">Transducer output modules</p>
<p>They are modules with the ability to produce a signal perceivable by
an human (pigment production, light, smell,... ) in response to Ubbit
presence. It’s composed by a R(Ubbit) coupled to a output emitter
device.</p>
</div>
</br>
<p class="title1">The Ubbit and its practical use in biodevice design.</p>
<hr
	style="float: left; color: #ABE107; background-color: #ABE107;">
</br>

<p>In order to understand and apply this standard, a definition of new
theoretical concepts is needed.</p>

<p>Firstly, a community is built with different strains (prokaryotic or
eukaryotic) exchanging information between them so that the whole
community can perform a specific function. The information would
probably be of a chemical nature, like the AHLs used by bacteria for the
quorum sensing, though we don’t reject other kinds of data (one of the
iGEM contestant teams has recently suggested using light as a way of
information transmision). We define any substance (or non-molecular
analogue) that acts as data for a couple of cells as BioBit or bbit.</p>

<p>In a community we’ll have input and output bbits besides the internal
communication bbits. In order to implement the Ubbit standard, a
community will have to emit output bbits that can be detected as input
information by another cell or group of cells, and induce a differential
gene expression in them, so that they can bio-synthetize new outputs
bbits for the next cell. So, if a community had three input bbits (a, b
and c), it would need three modified strains, named translators, that
could synthetize each substance when detecting Ubbit. With the
substances emited by the community after receiving the input information
it would happen the other way round; if the community produces two bbits
(d and e) there will be two strains that could specifically transform
each of the outputs bbits into Ubbit.</p>

<p>The community would be held in a physical stand; the community along
with its translator strains and the physical medium would constitute
what we call module. The modules would be as little black boxes of which
we only know their behaviour; their inputs, outputs and the function
they perform. They would be ready to be connected to modules created by
other bioengineers. Then we would have a population, a network of
interconnected modules exchanging information in Ubbits.</p>

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